Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs4648347

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3849191 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.484692 (128293/264690, TOPMED)
T=0.466651 (65152/139616, GnomAD)
C=0.41340 (32534/78698, PAGE_STUDY) (+ 16 more)
T=0.36665 (28732/78364, ALFA)
C=0.43675 (7320/16760, 8.3KJPN)
C=0.4347 (2177/5008, 1000G)
T=0.3250 (1456/4480, Estonian)
T=0.3077 (1186/3854, ALSPAC)
T=0.3096 (1148/3708, TWINSUK)
C=0.3440 (1008/2930, KOREAN)
C=0.4909 (1023/2084, HGDP_Stanford)
C=0.4153 (784/1888, HapMap)
T=0.327 (326/998, GoNL)
T=0.380 (228/600, NorthernSweden)
T=0.325 (128/394, SGDP_PRJ)
C=0.431 (93/216, Qatari)
T=0.12 (6/52, Ancient Sardinia)
T=0.29 (12/42, Siberian)
T=0.47 (19/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEP104 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 1 NC_000001.11:g.3849191T>C
GRCh37.p13 chr 1 NC_000001.10:g.3765755T>C
CEP104 RefSeqGene NG_046726.1:g.13043A>G
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.114-410A>G N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.222-410A…

XM_005244815.4:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.114-410A…

XM_011542474.3:c.114-410A>G

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.114-410A…

XM_017002918.2:c.114-410A>G

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.114-410A…

XM_017002919.2:c.114-410A>G

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.222-410A…

XM_024451101.1:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.222-410A…

XM_024451102.1:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.222-410A…

XM_024451103.1:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.222-410A…

XM_024451104.1:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.222-410A…

XM_024451106.1:c.222-410A>G

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c.222-410A…

XM_024451108.1:c.222-410A>G

N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 78364 T=0.36665 C=0.63335
European Sub 65238 T=0.32355 C=0.67645
African Sub 4414 T=0.7363 C=0.2637
African Others Sub 176 T=0.841 C=0.159
African American Sub 4238 T=0.7319 C=0.2681
Asian Sub 222 T=0.635 C=0.365
East Asian Sub 182 T=0.665 C=0.335
Other Asian Sub 40 T=0.50 C=0.50
Latin American 1 Sub 254 T=0.441 C=0.559
Latin American 2 Sub 1282 T=0.4360 C=0.5640
South Asian Sub 4978 T=0.5307 C=0.4693
Other Sub 1976 T=0.4656 C=0.5344


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 T=0.484692 C=0.515308
gnomAD - Genomes Global Study-wide 139616 T=0.466651 C=0.533349
gnomAD - Genomes European Sub 75652 T=0.32323 C=0.67677
gnomAD - Genomes African Sub 41792 T=0.74184 C=0.25816
gnomAD - Genomes American Sub 13592 T=0.39428 C=0.60572
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.3727 C=0.6273
gnomAD - Genomes East Asian Sub 3122 T=0.6794 C=0.3206
gnomAD - Genomes Other Sub 2136 T=0.4579 C=0.5421
The PAGE Study Global Study-wide 78698 T=0.58660 C=0.41340
The PAGE Study AfricanAmerican Sub 32514 T=0.73036 C=0.26964
The PAGE Study Mexican Sub 10810 T=0.46901 C=0.53099
The PAGE Study Asian Sub 8318 T=0.5831 C=0.4169
The PAGE Study PuertoRican Sub 7918 T=0.4720 C=0.5280
The PAGE Study NativeHawaiian Sub 4534 T=0.4826 C=0.5174
The PAGE Study Cuban Sub 4228 T=0.3877 C=0.6123
The PAGE Study Dominican Sub 3828 T=0.5408 C=0.4592
The PAGE Study CentralAmerican Sub 2450 T=0.4371 C=0.5629
The PAGE Study SouthAmerican Sub 1982 T=0.3739 C=0.6261
The PAGE Study NativeAmerican Sub 1260 T=0.4413 C=0.5587
The PAGE Study SouthAsian Sub 856 T=0.578 C=0.422
8.3KJPN JAPANESE Study-wide 16760 T=0.56325 C=0.43675
1000Genomes Global Study-wide 5008 T=0.5653 C=0.4347
1000Genomes African Sub 1322 T=0.7852 C=0.2148
1000Genomes East Asian Sub 1008 T=0.6597 C=0.3403
1000Genomes Europe Sub 1006 T=0.3588 C=0.6412
1000Genomes South Asian Sub 978 T=0.524 C=0.476
1000Genomes American Sub 694 T=0.367 C=0.633
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.3250 C=0.6750
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3077 C=0.6923
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3096 C=0.6904
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6560 C=0.3440
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.5091 C=0.4909
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.664 C=0.336
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.466 C=0.534
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.389 C=0.611
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.309 C=0.691
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.773 C=0.227
HGDP-CEPH-db Supplement 1 America Sub 216 T=0.444 C=0.556
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.53 C=0.47
HapMap Global Study-wide 1888 T=0.5847 C=0.4153
HapMap American Sub 768 T=0.509 C=0.491
HapMap African Sub 692 T=0.715 C=0.285
HapMap Asian Sub 254 T=0.602 C=0.398
HapMap Europe Sub 174 T=0.374 C=0.626
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.327 C=0.673
Northern Sweden ACPOP Study-wide 600 T=0.380 C=0.620
SGDP_PRJ Global Study-wide 394 T=0.325 C=0.675
Qatari Global Study-wide 216 T=0.569 C=0.431
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 52 T=0.12 C=0.88
Siberian Global Study-wide 42 T=0.29 C=0.71
The Danish reference pan genome Danish Study-wide 40 T=0.47 C=0.53
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C
GRCh38.p13 chr 1 NC_000001.11:g.3849191= NC_000001.11:g.3849191T>C
GRCh37.p13 chr 1 NC_000001.10:g.3765755= NC_000001.10:g.3765755T>C
CEP104 RefSeqGene NG_046726.1:g.13043= NG_046726.1:g.13043A>G
CEP104 transcript NM_014704.3:c.114-410= NM_014704.3:c.114-410A>G
CEP104 transcript NM_014704.4:c.114-410= NM_014704.4:c.114-410A>G
CEP104 transcript variant X1 XM_005244815.1:c.222-410= XM_005244815.1:c.222-410A>G
CEP104 transcript variant X2 XM_005244815.4:c.222-410= XM_005244815.4:c.222-410A>G
CEP104 transcript variant X3 XM_011542474.3:c.114-410= XM_011542474.3:c.114-410A>G
CEP104 transcript variant X7 XM_017002918.2:c.114-410= XM_017002918.2:c.114-410A>G
CEP104 transcript variant X8 XM_017002919.2:c.114-410= XM_017002919.2:c.114-410A>G
CEP104 transcript variant X1 XM_024451101.1:c.222-410= XM_024451101.1:c.222-410A>G
CEP104 transcript variant X4 XM_024451102.1:c.222-410= XM_024451102.1:c.222-410A>G
CEP104 transcript variant X5 XM_024451103.1:c.222-410= XM_024451103.1:c.222-410A>G
CEP104 transcript variant X6 XM_024451104.1:c.222-410= XM_024451104.1:c.222-410A>G
CEP104 transcript variant X9 XM_024451106.1:c.222-410= XM_024451106.1:c.222-410A>G
CEP104 transcript variant X10 XM_024451108.1:c.222-410= XM_024451108.1:c.222-410A>G
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

89 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396336 Feb 20, 2003 (111)
2 PERLEGEN ss24243900 Sep 20, 2004 (123)
3 ILLUMINA ss67352855 Dec 02, 2006 (127)
4 ILLUMINA ss67743290 Dec 02, 2006 (127)
5 ILLUMINA ss68232257 Dec 12, 2006 (127)
6 PERLEGEN ss68756700 May 18, 2007 (127)
7 ILLUMINA ss70812956 May 25, 2008 (130)
8 ILLUMINA ss71393462 May 18, 2007 (127)
9 ILLUMINA ss75524565 Dec 06, 2007 (129)
10 KRIBB_YJKIM ss84304101 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss87174829 Mar 23, 2008 (129)
12 1000GENOMES ss107949358 Jan 22, 2009 (130)
13 ILLUMINA-UK ss118453859 Feb 14, 2009 (130)
14 ENSEMBL ss137763858 Dec 01, 2009 (131)
15 ILLUMINA ss154304362 Dec 01, 2009 (131)
16 GMI ss154560007 Dec 01, 2009 (131)
17 ILLUMINA ss159481186 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss163739318 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss166009364 Jul 04, 2010 (132)
20 ILLUMINA ss173767962 Jul 04, 2010 (132)
21 BUSHMAN ss197925767 Jul 04, 2010 (132)
22 1000GENOMES ss218203493 Jul 14, 2010 (132)
23 1000GENOMES ss230404334 Jul 14, 2010 (132)
24 1000GENOMES ss238123181 Jul 15, 2010 (132)
25 BL ss252880868 May 09, 2011 (134)
26 GMI ss275691611 May 04, 2012 (137)
27 GMI ss283991101 Apr 25, 2013 (138)
28 PJP ss290498437 May 09, 2011 (134)
29 ILLUMINA ss482327626 May 04, 2012 (137)
30 ILLUMINA ss483489141 May 04, 2012 (137)
31 ILLUMINA ss535697783 Sep 08, 2015 (146)
32 TISHKOFF ss553734922 Apr 25, 2013 (138)
33 SSMP ss647536760 Apr 25, 2013 (138)
34 ILLUMINA ss780296593 Aug 21, 2014 (142)
35 ILLUMINA ss782187963 Aug 21, 2014 (142)
36 ILLUMINA ss832992617 Aug 21, 2014 (142)
37 ILLUMINA ss833583446 Aug 21, 2014 (142)
38 ILLUMINA ss835783225 Aug 21, 2014 (142)
39 EVA-GONL ss974796872 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1067627621 Aug 21, 2014 (142)
41 1000GENOMES ss1289453020 Aug 21, 2014 (142)
42 DDI ss1425693214 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1573860344 Apr 01, 2015 (144)
44 EVA_DECODE ss1584155603 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1599428060 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1642422093 Apr 01, 2015 (144)
47 EVA_SVP ss1712306806 Apr 01, 2015 (144)
48 HAMMER_LAB ss1793785769 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1917992392 Feb 12, 2016 (147)
50 ILLUMINA ss1958234864 Feb 12, 2016 (147)
51 JJLAB ss2019512416 Sep 14, 2016 (149)
52 USC_VALOUEV ss2147502756 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2159577137 Dec 20, 2016 (150)
54 TOPMED ss2321732000 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2624271978 Nov 08, 2017 (151)
56 ILLUMINA ss2632468733 Nov 08, 2017 (151)
57 GRF ss2697396836 Nov 08, 2017 (151)
58 GNOMAD ss2750975607 Nov 08, 2017 (151)
59 SWEGEN ss2986201886 Nov 08, 2017 (151)
60 ILLUMINA ss3021047730 Nov 08, 2017 (151)
61 BIOINF_KMB_FNS_UNIBA ss3023519849 Nov 08, 2017 (151)
62 TOPMED ss3067133632 Nov 08, 2017 (151)
63 CSHL ss3343289193 Nov 08, 2017 (151)
64 ILLUMINA ss3626012050 Oct 11, 2018 (152)
65 ILLUMINA ss3630508034 Oct 11, 2018 (152)
66 ILLUMINA ss3637733790 Oct 11, 2018 (152)
67 ILLUMINA ss3638888286 Oct 11, 2018 (152)
68 ILLUMINA ss3639757013 Oct 11, 2018 (152)
69 ILLUMINA ss3641567889 Oct 11, 2018 (152)
70 ILLUMINA ss3642748003 Oct 11, 2018 (152)
71 ILLUMINA ss3643810935 Oct 11, 2018 (152)
72 ILLUMINA ss3651370384 Oct 11, 2018 (152)
73 EGCUT_WGS ss3654303072 Jul 12, 2019 (153)
74 EVA_DECODE ss3686047899 Jul 12, 2019 (153)
75 ILLUMINA ss3724990969 Jul 12, 2019 (153)
76 ACPOP ss3726740394 Jul 12, 2019 (153)
77 EVA ss3745755848 Jul 12, 2019 (153)
78 PAGE_CC ss3770780910 Jul 12, 2019 (153)
79 KHV_HUMAN_GENOMES ss3798777494 Jul 12, 2019 (153)
80 EVA ss3825994205 Apr 25, 2020 (154)
81 EVA ss3836384302 Apr 25, 2020 (154)
82 EVA ss3841788479 Apr 25, 2020 (154)
83 HGDP ss3847322579 Apr 25, 2020 (154)
84 SGDP_PRJ ss3848070231 Apr 25, 2020 (154)
85 KRGDB ss3892931908 Apr 25, 2020 (154)
86 EVA ss3984774971 Apr 25, 2021 (155)
87 EVA ss4016890130 Apr 25, 2021 (155)
88 TOPMED ss4437314756 Apr 25, 2021 (155)
89 TOMMO_GENOMICS ss5142203094 Apr 25, 2021 (155)
90 1000Genomes NC_000001.10 - 3765755 Oct 11, 2018 (152)
91 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3765755 Oct 11, 2018 (152)
92 Genetic variation in the Estonian population NC_000001.10 - 3765755 Oct 11, 2018 (152)
93 The Danish reference pan genome NC_000001.10 - 3765755 Apr 25, 2020 (154)
94 gnomAD - Genomes NC_000001.11 - 3849191 Apr 25, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000001.10 - 3765755 Apr 25, 2020 (154)
96 HGDP-CEPH-db Supplement 1 NC_000001.9 - 3755615 Apr 25, 2020 (154)
97 HapMap NC_000001.11 - 3849191 Apr 25, 2020 (154)
98 KOREAN population from KRGDB NC_000001.10 - 3765755 Apr 25, 2020 (154)
99 Northern Sweden NC_000001.10 - 3765755 Jul 12, 2019 (153)
100 The PAGE Study NC_000001.11 - 3849191 Jul 12, 2019 (153)
101 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 3765755 Apr 25, 2021 (155)
102 Qatari NC_000001.10 - 3765755 Apr 25, 2020 (154)
103 SGDP_PRJ NC_000001.10 - 3765755 Apr 25, 2020 (154)
104 Siberian NC_000001.10 - 3765755 Apr 25, 2020 (154)
105 8.3KJPN NC_000001.10 - 3765755 Apr 25, 2021 (155)
106 TopMed NC_000001.11 - 3849191 Apr 25, 2021 (155)
107 UK 10K study - Twins NC_000001.10 - 3765755 Oct 11, 2018 (152)
108 ALFA NC_000001.11 - 3849191 Apr 25, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs17404414 Oct 07, 2004 (123)
rs60083846 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638888286, ss3639757013, ss3643810935 NC_000001.8:3788911:T:C NC_000001.11:3849190:T:C (self)
471, ss87174829, ss107949358, ss118453859, ss163739318, ss166009364, ss197925767, ss252880868, ss275691611, ss283991101, ss290498437, ss482327626, ss1584155603, ss1712306806, ss3642748003, ss3847322579 NC_000001.9:3755614:T:C NC_000001.11:3849190:T:C (self)
121090, 54357, 41320, 1367578, 23475, 109302, 25259, 898, 34322, 87211, 19110, 172401, 54357, ss218203493, ss230404334, ss238123181, ss483489141, ss535697783, ss553734922, ss647536760, ss780296593, ss782187963, ss832992617, ss833583446, ss835783225, ss974796872, ss1067627621, ss1289453020, ss1425693214, ss1573860344, ss1599428060, ss1642422093, ss1793785769, ss1917992392, ss1958234864, ss2019512416, ss2147502756, ss2321732000, ss2624271978, ss2632468733, ss2697396836, ss2750975607, ss2986201886, ss3021047730, ss3343289193, ss3626012050, ss3630508034, ss3637733790, ss3641567889, ss3651370384, ss3654303072, ss3726740394, ss3745755848, ss3825994205, ss3836384302, ss3848070231, ss3892931908, ss3984774971, ss4016890130, ss5142203094 NC_000001.10:3765754:T:C NC_000001.11:3849190:T:C (self)
871360, 2902, 2379, 573586, 921091, 10060509006, ss2159577137, ss3023519849, ss3067133632, ss3686047899, ss3724990969, ss3770780910, ss3798777494, ss3841788479, ss4437314756 NC_000001.11:3849190:T:C NC_000001.11:3849190:T:C (self)
ss6396336, ss24243900, ss67352855, ss67743290, ss68232257, ss68756700, ss70812956, ss71393462, ss75524565, ss84304101, ss137763858, ss154304362, ss154560007, ss159481186, ss173767962 NT_004350.19:3244386:T:C NC_000001.11:3849190:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs4648347

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad